sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2004-02-04
| Name: | Gag-Pol polyprotein |
|---|---|
| ID: | POL_HV1B1 |
| AC: | P03366 |
| Organism: | Human immunodeficiency virus type 1 group M subtype B |
| Reign: | Viruses |
| TaxID: | 11678 |
| EC Number: | 2.7.7.49 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 94 % |
| B | 6 % |
| B-Factor: | 70.476 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.349 | 648.000 |
| % Hydrophobic | % Polar |
|---|---|
| 63.02 | 36.98 |
| According to VolSite | |
| HET Code: | ADB |
|---|---|
| Formula: | C16H10Cl2N6O |
| Molecular weight: | 373.196 g/mol |
| DrugBank ID: | DB07343 |
| Buried Surface Area: | 73.57 % |
| Polar Surface area: | 109.74 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 144.321 | -24.7569 | 73.4806 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| CL2 | CG | PRO- 95 | 3.38 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 100 | 3.27 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 100 | 3.74 | 0 | Hydrophobic |
| N5 | O | LYS- 101 | 2.82 | 174.84 | H-Bond (Ligand Donor) |
| N2 | N | LYS- 101 | 3.26 | 157.27 | H-Bond (Protein Donor) |
| C11 | CG | LYS- 103 | 4.09 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 106 | 3.48 | 0 | Hydrophobic |
| CL6 | CG2 | VAL- 179 | 3.7 | 0 | Hydrophobic |
| CL2 | CD1 | TYR- 181 | 3.55 | 0 | Hydrophobic |
| CL6 | CB | TYR- 181 | 4.01 | 0 | Hydrophobic |
| C1 | CB | TYR- 181 | 3.32 | 0 | Hydrophobic |
| C5 | CD2 | TYR- 188 | 3.25 | 0 | Hydrophobic |
| C5 | CB | TYR- 188 | 3.36 | 0 | Hydrophobic |
| CL2 | CH2 | TRP- 229 | 4.25 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 234 | 4.28 | 0 | Hydrophobic |
